Opportunities and challenges in design and optimization of protein function

D Listov, CA Goverde, BE Correia… - … Reviews Molecular Cell …, 2024 - nature.com
The field of protein design has made remarkable progress over the past decade. Historically,
the low reliability of purely structure-based design methods limited their application, but …

Machine learning-guided protein engineering

P Kouba, P Kohout, F Haddadi, A Bushuiev… - ACS …, 2023 - ACS Publications
Recent progress in engineering highly promising biocatalysts has increasingly involved
machine learning methods. These methods leverage existing experimental and simulation …

Automated in vivo enzyme engineering accelerates biocatalyst optimization

E Orsi, L Schada von Borzyskowski, S Noack… - Nature …, 2024 - nature.com
Achieving cost-competitive bio-based processes requires development of stable and
selective biocatalysts. Their realization through in vitro enzyme characterization and …

Machine learning-guided co-optimization of fitness and diversity facilitates combinatorial library design in enzyme engineering

K Ding, M Chin, Y Zhao, W Huang, BK Mai… - Nature …, 2024 - nature.com
The effective design of combinatorial libraries to balance fitness and diversity facilitates the
engineering of useful enzyme functions, particularly those that are poorly characterized or …

Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments

M Gantz, S Neun, EJ Medcalf, LD van Vliet… - Chemical …, 2023 - ACS Publications
Novel and improved biocatalysts are increasingly sourced from libraries via experimental
screening. The success of such campaigns is crucially dependent on the number of …

The crucial role of methodology development in directed evolution of selective enzymes

G Qu, A Li, CG Acevedo‐Rocha, Z Sun… - Angewandte Chemie …, 2020 - Wiley Online Library
Directed evolution of stereo‐, regio‐, and chemoselective enzymes constitutes a unique way
to generate biocatalysts for synthetically interesting transformations in organic chemistry and …

Thermal stability enhancement: Fundamental concepts of protein engineering strategies to manipulate the flexible structure

M Rahban, S Zolghadri, N Salehi, F Ahmad… - International journal of …, 2022 - Elsevier
Increasing the temperature by just a few degrees may lead to structural perturbation or
unfolding of the protein and consequent loss of function. The concepts of flexibility and …

Unravelling and reconstructing the biosynthetic pathway of bergenin

R Yan, B **e, K **e, Q Liu, S Sui, S Wang… - Nature …, 2024 - nature.com
Bergenin, a rare C-glycoside of 4-O-methyl gallic acid with pharmacological properties of
antitussive and expectorant, is widely used in clinics to treat chronic tracheitis in China …

Advancing enzyme's stability and catalytic efficiency through synergy of force-field calculations, evolutionary analysis, and machine learning

A Kunka, SM Marques, M Havlasek, M Vasina… - ACS …, 2023 - ACS Publications
Thermostability is an essential requirement for the use of enzymes in the bioindustry. Here,
we compare different protein stabilization strategies using a challenging target, a stable …

[HTML][HTML] Engineering enzyme access tunnels

P Kokkonen, D Bednar, G Pinto, Z Prokop… - Biotechnology …, 2019 - Elsevier
Enzymes are efficient and specific catalysts for many essential reactions in biotechnological
and pharmaceutical industries. Many times, the natural enzymes do not display the catalytic …